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A single logic operation following DNA strand displacement methodology requires approximately 30 minutes time to be executed. Furthermore, the concentration of an output molecule released from a gate cannot exceed that of the gate molecule. These are the major two disadvantages of the model for performing logic operations which has been described in Section 2.5.2. To overcome these drawbacks, Hirose et al. [9] proposed a new model for construction of the combinatorial circuits using DNA polymerase and nicking enzyme. Using this method, the logic gates can be computed quickly and the output molecules can be amplified.

In this model, for each Boolean variable a, two DNA strands A and NA are prepared. The existence of A in the solution implies the evaluation of the Boolean variable a as 1 and the existence of NA in the solution implies the evaluation of the Boolean variable a as 0. Thus, the strands A and NA cannot exist at the same time in the solution. In this model the negation strand NA can be used to implement NOT gate. Now, it is assumed that the nicking enzyme recognizes a double-stranded DNA sequences and cleaves the 3’ end of the lower strand R* only.

The implementations of the above-mentioned reactions using DNA polymerase and nicking enzyme are illustrated in the next subsections. To implement logic circuit the following basic abstract level chemical reactions are required;